Streptomyces sedi (DSM 41942, CCTCC AA 208020, JCM 16909)

Name: Streptomyces sedi (DSM 41942, CCTCC AA 208020, JCM 16909)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16457

Type strain

Culture col. no. DSM 41942 CCTCC AA 208020 JCM 16909 YIM 65188

NCBI tax ID(s) 555059

Special Collections DSMZ JCM Wink compendium Literature strains

History <- S.-K. Tang, YIM; YIM 65188 <- J. Li DSM 41942 <-- S.-K. Tang <-- J. Li YIM 65188.

Links

Streptomyces sedi DSM 41942 is a spore-forming, rod-shaped bacterium that was isolated from surface-sterilized tissues of Sedum sp..

spore-forming rod-shaped genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 403359

JCM 16909,DSM 41942

@ref 20215

Last LPSN update 2026-02-09 11:21:58

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Streptomyces

Species Streptomyces sedi

Full scientific name Streptomyces sedi Li et al. 2009

Morphology

Cell morphology

@ref	Confidence	Cell shape	Gram stain
29155		rod-shaped
125438	90.5
125438	90.23		positive
125439	100		positive
125439	96.6

Colony morphology

@ref	Colony color	Incubation period	Medium used
19830	Light ivory	10-14 days	ISP 2
19830		10-14 days	ISP 3
19830		10-14 days	ISP 4
19830		10-14 days	ISP 5
19830		10-14 days	ISP 6
19830		10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19830		ISP 2
19830		ISP 3
19830		ISP 4
19830		ISP 5
19830		ISP 6
19830		ISP 7

Pigmentation

29155

Productionno

Multimedia

@ref:	15710
multimedia content:	DSM_41942.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_41942.jpg
caption:	Medium 987 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
15710	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19830	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19830	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19830	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19830	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19830	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19830	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
15710	STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)	Medium recipe at MediaDive	Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water
15710	ISP2 MEDIUM (DSMZ Medium 987)	Medium recipe at MediaDive	Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
15710	ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)	Medium recipe at MediaDive	Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
15710	positive	growth	28
19830	positive	optimum	28
29155	positive	growth	15-37
29155	positive	optimum	26
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH
29155	positive	optimum	7.5
29155	positive	growth	7.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	99.8

Spore formation

@ref	Spore formation	Confidence
29155
125438		90.878
125439		96.2

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29155	NaCl	positive	growth	0-5 %
29155	NaCl	positive	optimum	2.5 %

Observation

@ref	Observation
29155	aggregates in chains
67770	quinones: MK-11(H₆), MK-10(H₆), MK-10(H₈), MK-11(H₈)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29155	16449 ChEBI	alanine	+	carbon source
29155	17057 ChEBI	cellobiose	+	carbon source
29155	4853 ChEBI	esculin	+	hydrolysis
29155	28757 ChEBI	fructose	+	carbon source
29155	27570 ChEBI	histidine	+	carbon source
29155	17306 ChEBI	maltose	+	carbon source
29155	26271 ChEBI	proline	+	carbon source
29155	17822 ChEBI	serine	+	carbon source
29155	53424 ChEBI	tween 20	+	carbon source
29155	53423 ChEBI	tween 40	+	carbon source
29155	53426 ChEBI	tween 80	+	carbon source
29155	16199 ChEBI	urea	+	carbon source

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	+	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
29155	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	+		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68382	trypsin	+	3.4.21.4	from API zym
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
19830	not determinedn.d.	+	+	+	+	+	+	+	+	-	+	+	-	+	-	+	+	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host	#Plants	#Shrub (Scrub)
#Host Body-Site	#Plant	#Sterilized plant part

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
15710	surface-sterilized tissues of Sedum sp.	Sedum	Yunnan province	China	CHN	Asia
67770	Surface-sterilized tissue of Sedum sp.	Sedum sp.	Yunnan Province, south-west China	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence EU925562 (>99% sequence identity) for Streptomyces from Microbeatlas

Aquatic Samples	68
Soil Samples	177
Animal Samples	307
Plant Samples	61
Total Samples	613

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15710	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM633501v1 assembly for Streptomyces sedi JCM 16909	contig	GCA_006335015	555059.3	2990044586	555059	66.68
124043	ASM3953702v1 assembly for Streptomyces sedi JCM 16909	scaffold	GCA_039537025			555059	13.38

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15710	Streptomyces sedi strain YIM 65188 16S ribosomal RNA gene, partial sequence	EU925562	1440		555059

GC content

@ref	GC-content (mol%)	Method
15710	71.0	high performance liquid chromatography (HPLC)
29155	71
67770	71	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Streptomyces sedi JCM 16909
NCBI: GCA_006335015

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	96.20	no
125439	motility	BacteriaNetⓘ	no	96.60	no
125439	gram_stain	BacteriaNetⓘ	positive	100.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptomyces sedi strain JCM 16909
PATRIC: 555059.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.23	no
125438	anaerobic	anaerobicⓘ	no	96.38	no
125438	spore-forming	spore-formingⓘ	yes	90.88	yes
125438	aerobic	aerobicⓘ	yes	89.84	no
125438	thermophilic	thermophileⓘ	no	90.82	yes
125438	flagellated	motile2+ⓘ	no	90.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome mining for drug discovery: cyclic lipopeptides related to daptomycin.	Baltz RH.	J Ind Microbiol Biotechnol	10.1093/jimb/kuab020	2021
	Pattern-Based Genome Mining Guides Discovery of the Antibiotic Indanopyrrole A from a Marine Streptomycete.	Sweeney D, Bogdanov A, Chase AB, Castro-Falcon G, Trinidad-Javier A, Dahesh S, Nizet V, Jensen PR.	J Nat Prod	10.1021/acs.jnatprod.4c00934	2024
Metabolism	Streptomyces strains producing mitochondriotoxic antimycin A found in cereal grains.	Rasimus-Sahari S, Mikkola R, Andersson MA, Jestoi M, Salkinoja-Salonen M.	Int J Food Microbiol	10.1016/j.ijfoodmicro.2015.11.007	2016
Phylogeny	Multiple strain analysis of Streptomyces species from Philippine marine sediments reveals intraspecies heterogeneity in antibiotic activities.	Tenebro CP, Trono DJVL, Vicera CVB, Sabido EM, Ysulat JA, Macaspac AJM, Tampus KA, Fabrigar TAP, Saludes JP, Dalisay DS.	Sci Rep	10.1038/s41598-021-96886-4	2021
Enzymology	New ikarugamycin derivatives with antifungal and antibacterial properties from Streptomyces zhaozhouensis.	Lacret R, Oves-Costales D, Gomez C, Diaz C, de la Cruz M, Perez-Victoria I, Vicente F, Genilloud O, Reyes F.	Mar Drugs	10.3390/md13010128	2014
	Streptomyces profundus sp. nov., a novel marine actinobacterium isolated from deep-sea sediment of Madeira Archipelago, Portugal.	Ribeiro I, Correia S, Blumel M, Albuquerque P, Gorb SN, Mendes MV, Tasdemir D, Mucha AP, Carvalho MF.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006341	2024
Phylogeny	Streptomyces mimosae sp. nov., an endophytic actinomycete isolated from the root of Mimosa pudica in Thailand.	Klykleung N, Yuki M, Kudo T, Ohkuma M, Phongsopitanun W, Inahashi Y, Matsumoto A, Tanasupawat S	Int J Syst Evol Microbiol	10.1099/ijsem.0.004170	2020
Phylogeny	Streptomyces triticagri sp. nov. and Streptomyces triticirhizae sp. nov., two novel Actinobacteria isolated from the rhizosphere soil of wheat (Triticum aestivum L.).	Han C, Yu Z, Zhao J, Shi H, Hu J, Yu B, Song J, Shen Y, Xiang W, Wang X	Int J Syst Evol Microbiol	10.1099/ijsem.0.003727	2020
Phylogeny	Streptomyces burgazadensis sp. nov., isolated from soil.	Saricaoglu S, Isik K, Veyisoglu A, Saygin H, Cetin D, Guven K, Sproer C, Klenk HP, Sahin N	Int J Syst Evol Microbiol	10.1099/ijs.0.065870-0	2014
Phylogeny	Streptomyces zhaozhouensis sp. nov., an actinomycete isolated from candelabra aloe (Aloe arborescens Mill).	He H, Liu C, Zhao J, Li W, Pan T, Yang L, Wang X, Xiang W	Int J Syst Evol Microbiol	10.1099/ijs.0.056317-0	2013
Phylogeny	Streptomyces hoynatensis sp. nov., isolated from deep marine sediment.	Veyisoglu A, Sahin N	Int J Syst Evol Microbiol	10.1099/ijs.0.055640-0	2013
Phylogeny	Streptomyces sedi sp. nov., isolated from surface-sterilized roots of Sedum sp.	Li J, Zhao GZ, Qin S, Zhu WY, Xu LH, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.007534-0	2009

References

#15710	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 41942
#19830	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#25579	IJSEM 1492 2009 ( DOI 10.1099/ijs.0.007534-0 , PubMed 19502341 )
#29155	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25579
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Streptomyces sedi (DSM 41942, CCTCC AA 208020, JCM 16909)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_006335015

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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